Huaijun Zhou, Ph.D.

Huaijun Zhou

Professor and Chancellor’s Fellow, Department of Animal Science
Director of USAID Feed the Future Innovation Lab for Genomics to Improve Poultry

2247 Meyer Hall


  • B.S., Animal Science, Yangzhou University.
  • M.S., Animal Breeding and Genetics, Yangzhou University.
  • M.S., Bioinformatics and Computational Biology, Iowa State University.
  • Ph.D., Immunogenetics and Molecular Genetics Iowa State University.

Honors and Awards

  • 2020 Chancellor’s Awards for International Engagement
  • 2018 Zoetis Fundamental Science Award (PSA)
  • 2016 - Evonik Degussa Award for Achievement in Poultry Science
  • 2014 - Chancellor’s Fellow
  • 2013 - The American Association of Immunologists Early Career Faculty Travel Award
  • 2011 - PSA Early Achievement Award for Research
  • 2010 - Hy-Line International Research Award
  • 2009 - Big 12 Faculty Fellowship
  • 2009 - Outstanding Overseas Young Investigator Award, NSF China
  • 2004 - Natural Sciences and Engineering Research Council of Canada (NSERC) Fellowship
  • 2002 - Research Excellence Award, Iowa State University   


Research Projects

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  • USDA NIFA project: Functional Annotation of Regulatory Elements in Livestock Species. This project is one of pilot projects of FAANG consortium (www. The overall goal of this project is to generate a comprehensive resource of functional genomic elements for the chicken, cattle, and pig genomes. Our specific goals are:  
  1. Annotate chromatin states corresponding to DNase hypersensitivity, four histone modifications, and one transcription factor
  2. Annotate promoters, enhancers, and silencers by integrating information from RNA-seq, DNAse-seq, and ChIP-seq against four histone modifications and one transcription factor.
  3. Freely distribute all raw and annotated data via UCSC Genome Browser and Ensembl.


  • NIH-NIFA Dual Purpose with Dual Benefits project: Development of Colonization Resistance in Chicks.
  • Our long-range goal is to understand the mechanisms that govern the interactions between the host and its gut-associated microbial communities. The objectives of this application are to study the mechanism of colonization resistance and devise strategies to prevent a bloom of Proteobacteria after hatching.
    • Specific Aim 1: Determine the mechanism by which obligate anaerobic bacteria confer colonization resistance against Proteobacteria in newly hatched chicks
    • Specific Aim 2: Determine whether a treatment that enhances colonization resistance accelerates development of a mature microbial community structure in newly hatched chicks.

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Graduate Groups

Courses Taught

  • Animal Health and Disease, offered in Spring (ANS 150)
  • Avian Biology, offered in Spring (AVS 100)


A full list of current and past lab members.

Selected Publications

Dr. Huaijun Zhou has published a total of 104 peer-reviewed papers, two book chapters and 200 peer-reviewed abstract and/or meeting proceedings. Here are his representative publications::

Litvak Y., K.K.Z. Mon, H. Nguyen, G. Chanthavixay, M. Liou, E. M. Velazquez, L. Kutter, M. A. Alcantara, M. X. Byndloss, C.R. Tiffany, G. T. Walker, F. Faber, Y. Zhu, D. N. Bronner, A. J. Byndloss, R. M. Tsolis, H. Zhou. A. J. Baumler. 2019. Commensal Enterobacteriaceae protect against Salmonella colonization by competing for oxygen. Cell Host & Microbes 25, 1-12

Saelao, P., Y. Wang, G. Chanthavixay, V. Yu, J. Dekkers, R. Gallardo, T.R. Kelly, S.J. Lamont. Zhou, H. 2018. Integrated proteomic and transcriptomic analysis of differential expression of chicken lung tissue in response to NDV infection during heat stress. Genes 9, 579; doi:10.3390/genes9120579

Kim, T.H. and H. Zhou. 2018. Overexpression of chicken IRF7 increased viral replication and programmed cell death to the avian influenza virus infection through TGF-beta/FoxO signaling axis in DF-1. Frontiers in Genetics. doi: 10.3389/fgene.2018.00415.

Saelao, P., Y. Wang, K. Chanthavixay, J. Dekkers, R. Gallardo, T.R. Kelly, S.J. Lamont. H. Zhou. 2018. Novel insights into the host immune response of chicken Harderian gland tissue during Newcastle disease virus infection and heat treatment. BMC Veterinary Research

Kern, C. P. P. Saelao, Y. Wang, M. Halstead, J. L. Chitwood, I. Korf, M. Delany, H. Cheng, J. F. Medrano, A. Van Eenennaam, C. W. Ernst. J. Ross, H. Zhou. 2018. Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species. BMC Genomics

K. Rowland. Wolc. J. H. Zhou, R. Gallardo, T. Kelly, A. Dekkers, Lamont. S.J. 2018. Genome-wide association study of a commercial egg laying line challenged with Newcastle disease virus. Front. Genet., |

Wilson B. K, T. Kelly, D.A. Bunn, and H. Zhou. 2018. Key criteria and models for implementing a sustainable chicken breeding and distribution program for smallholder poultry producers. Livestock Research for Rural Development. 30 (4), Article #67. Retrieved April 13, 2018,

Zhang J, Kaiser MG, Deist MS, Gallardo RA, Bunn DA, Kelly TR, Dekkers JCM, Zhou H, Lamont SJ. Transcriptome Analysis in Spleen Reveals Differential Regulation of Response to Newcastle Disease Virus in Two Chicken Lines. Sci Rep. 2018 Jan 19;8(1):1278. doi: 10.1038/s41598-018-19754-8.

Zar Mon, K. K., P. Saelao, M. M. Halstead, G. Chanthavixay, H.-C. Chang, L. Garas, E. A Maga and H. Zhou. 2016. Salmonella enterica serovars Enteritidis infection alters the indigenous microbiota diversity in young layer chicks. Front. Vet. Sci. - Veterinary Infectious Diseases. 2:61. doi: 10.3389/fvets.2015.00061.

Li J, Li R, Wang Y, Hu X, Zhao Y, Li L, Feng C, Gu X, Liang F, Lamont S, Hu S, Zhou H*, Li N. 2015. Genome-wide DNA methylome variation in two genetically distinct chicken lines using MethylC-seq. BMC Genomics, 16 :851 (23 October 2015)

Kim, T.H, H. Zhou. 2015. Functional Analysis of Chicken IRF7 in Response to dsRNA Analog Poly(I:C) by Integrating Overexpression and Knockdown: 10.1371/journal.pone.0133450.

Schmid M. et al. H. Zhou. 2015.Third Report on Chicken Genes and Chromosomes.  Cytogenet Genome Res 145:78-179 (DOI:10.1159/000430927).

 Leif, A. et al. H. Zhou, The FAANG Consortium.  2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16:57. DOI: 10.1186/s13059-015-0622-4

Abernathy, J., Li, X., Jia, X., Chou, W., Lamont, S.J., Crooijmans, R., and Zhou, H. 2014. Copy number variation in Fayoumi and Leghorn chickens analyzed using array comparative genomic hybridization. Animal Genetics. doi: 10.1111/age.12141.

Wang Y, Lupiani B, Reddy S, S. J. Lamont, Zhou H. 2014. RNA-seq analysis revealed novel genes and signaling pathway associated with disease resistance to avian influenza virus infection in chickens. Poultry Science. 93(2):485-93. doi: 10.3382/ps.2013-03557.

Wang, Y., V. Brahmakshatriya, B. Lupiani, S. M Reddy, B. Soibam, A. L Benham, P. Gunaratne, H.Liu, M. Trakooljul, N. Ing, R. Okimoto and H. Zhou 2012. Integrated Analysis of microRNA Expression and mRNA Transcriptome in Lungs of Avian Influenza Virus Infected Broilers. BMC Genomics 13:278 (Highly assessed)

Wang Y, N. Ghaffari, C. D. Johnson, U. M. Braga-Neto, H. Wang, R. Chen, H. Zhou. 2011 Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens. BMC Bioinformatics 12: doi:10.1186/1471-2105-12-S10-S5.

Li X., C. L. Swaggerty, M. H. Kogut, H. Chiang, Y. Wang, K. J. Genovese, H. He, H. Zhou. 2010. Gene expression profiling of the local cecal response of genetic chicken lines that differ in their susceptibility to Campylobacter jejuni colonization. PLoS ONE 5(7): e11827. doi:10.1371/journal.pone.0011827

Wang Y., V. Brahmakshatriya, B. Lupiani, S. Reddy, B. Yoon, H. Zhu, P. Gunaratne, R. Chen, J. Wang, H. Zhou. 2009. Identification of differentially expressed microRNAs In chicken lung and trachea with avian influenza virus infection by Solexa Sequencer. BMC Genomics 10:512. (Highly assessed)

Chiang, H.I., C. Swaggerty, M. Kogut, S. Dowd, X. Li, I. Pevzner, and H. Zhou. 2008. Gene expression profiling in chicken heterophils with Salmonella enteritidis stimulation using a chicken 44K Agilent microarray. BMC Genomics 9:526.

Li, X.Y, H.I. Chiang, J. Zhu, S. Dowd and H. Zhou. 2008. Characterization of newly developed chicken 44K Agilent microarray. BMC Genomics 9:60. (Highly assessed)

Wong, G. K., H Zhou et al.  2004.  A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.  Nature 432:717-722.